Marshall became the head coach at Winthrop University in 1998, and led the Winthrop Eagles men's basketball team to seven NCAA tournament appearances and transformed a previously undistinguished program into a mid-major powerhouse. In his first season at Winthrop in 1998–99, he compiled a record of 19–8 (9–1 in Big South Conference play), coaching the Eagles to their first regular season Big South title. They went on to win the Big South Conference Tournament, earning the Eagles their first-ever bid to the NCAA Tournament. As a No. 16 seed, the team lost to the No. 1 seed Auburn Tigers in the first round, 80–41.[4]

During his nine seasons at Winthrop, Marshall coached the team to six regular season titles (1999, 2002, 2003, 2005, 2006, 2007), seven Big South Tournament titles (1999, 2000, 2001, 2002, 2005, 2006, 2007), six 20-win seasons (1999, 2000, 2003, 2005, 2006, 2007), and was named Big South Coach of the Year four times (1999, 2003, 2005, 2007). In 2006, he became the all-time winningest coach in Winthrop men's basketball history.[2] During the 2006–07 season, Marshall became the first coach in the history of the Big South Conference to have his team go undefeated in conference play.

The 2006 NCAA Tournament matched No. 15 seed Winthrop against the No. 2 seed Tennessee Volunteers, the Southeastern Conference Eastern Division champion, in the first round. Winthrop led for much of the game, only to lose 63-61 on a long jump shot with 2.9 seconds remaining.[5] In 2007, Marshall became the first Big South coach to win an NCAA first round tournament game by defeating No. 6 seed Notre Dame.[6]

Marshall accepted Wichita State University's offer to coach its Wichita State Shockers men's basketball team on April 14, 2007[9] In his fourth season at WSU, Marshall lead the Shockers to the NIT Championship, defeating Alabama in the finals.[10] Under Marshall, Wichita State broke into the AP Top 25 poll on February 13, 2012, the first time since December 25, 2006,[11] and only the second time since 1983.[12] In 2012, Wichita State made its first appearance in the NCAA tournament since the 2005–06 season, receiving an at-large bid.[13] The Shockers were matched as a No. 5 seed versus the No. 12 seed VCU Rams, but the Shockers lost 62–59.[13] In the 2012-2013 season, Marshall led the Shockers to their first Final Four since 1965, defeating the AP #1, #7, and #20 teams in the country to win the West Regional.

In 2013-14, Marshall led Wichita State to arguably the greatest season in school history. The Shockers steamrolled through the regular season, becoming the second Division I team to start a regular season with 30 consecutive wins (31-0). They rose as high as second in both major polls in late February, the highest that a Shocker team has been ranked since 1981. On March 9, 2014, Wichita State finished their regular season and the Missouri Valley Conference Tournament with a record of 34-0, heading into the NCAA Tournament undefeated. This 34-0 record ties a NCAA Division I Men's basketball record, held by the University of Nevada Las Vegas, set in 1991. Wichita State later went on to win their first game of the 2014 NCAA Tournament versus Cal Poly 64-37. The Shockers were 35-0, becoming the first team in Men's Division I basketball history to start with 35 wins and zero loses. In the third round of the tournament they squared off against Kentucky. Wichita State lost the game 78-76, ending their perfect run. They finished the 2013-14 season at 35-1.